Background: Chronic pediatric headache disorders are pervasive, debilitating, and associated with high rates of comorbid anxiety disorders. The combination of headaches and anxiety presents unique challenges for clinicians. Cognitive behavioral therapy (CBT) is a promising treatment for pediatric headache, however, available treatments fail to adequately address comorbid psychopathology resulting in less than optimal response rates. Objective: This case study illustrates the use of a family-based CBT for treating comorbid pediatric headache and anxiety disorders. Methods: A 10 year old boy with chronic daily headache was evaluated and treated as part of the Children's Headache and Anxiety Management Program (CHAMP). The patient and his parents were evaluated by an independent evaluator (IE) at pre- and post-treatment and one-month follow-up. Evaluations consisted of structured interviews as well as parent and child self-report measures of headache and anxiety symptoms and impairment. At baseline the child met diagnostic criteria for chronic headache disorder, separation (SAD), and generalized anxiety disorders (GAD), and had significant symptoms of obsessive-compulsive disorder (OCD). Treatment included 8 conjoint sessions of CBT. Results: Post-treatment evaluation revealed a significant reduction in headache-related severity and disability (but not frequency), and loss of initial GAD (but not SAD) diagnosis. By the one-month follow-up, the child no longer met criteria for any anxiety disorder and was no longer disabled by headaches. The case highlights how CHAMP may be effective in reducing headache and anxiety symptoms and associated impairment. Conclusions: This case illustrates the challenges in treating this population and suggests specific interventions that might enhance treatment outcome.